Citadel Noire
by Wargrave
Summary: Mass Effect AU. Decades ago, an alien prisoner ship crashed into Earth, and the alien aboard have moved into a nearby city called Citadel, and they're there to stay. An uneasy peace exists, but when a murder occurs, tensions arise. Jonathan Phoenix, a private investigator, is called upon to solve the murder and avoid open war. Rated M for swearing and violence.
1. Chapter 1

Citadel Noire

Prologue

It was the same every night.

Every night, while he slept, his brain tormented him with the day that everything changed.

He could recall the images with perfect clarity; her hand in his as they ran, the sounds of bullets flying through the air followed by the sounds of their ugly impacts on ground or flesh, the smell of fear exuding out of himself.

The sound of her cry as her hand left his and she fell to the ground.

He had run back to her where she lay face down on the ground, had fallen to his knees and rolled her over, dragging her onto him, one arm behind her head, her back on his thighs, as his other hand tried to staunch the blood pumping from the hole in her chest.

In vain.

The scene ended the same way every time: her hand moving slowly and smoothly to his face while the rest of her body shuddered and twitched, her breath coming in weak, blood filled gasps. He leaned his face into her palm, his tears streaking hot and fast onto the back of her hand and down her arm. Her mouth moved, and he leaned in close to hear her over the sound of fighting.

"I-I… love you…"

Just like that, the scene ends; before he can say it too, before he can say goodbye one last time. The scene ends with the graying in her eyes and the sound of his anguish tearing its way out of his throat, his cry drowning out the world with its intensity.

As if his own cry could drag him out of the chasm of his dreams, Jonathan Phoenix wakes up with a start. 

Chapter one

Jonathan sat alone in his apartment, staring out the window without seeing anything. He had turned his only chair to the window so he could watch the city from his fourth story apartment, marveling at the sounds and sights it provided him every day and night. He sat motionless for the most part, with the exception of his hands; with the fingers of his left hand, he fidgeted slowly with a worn golden band on his fourth finger, spinning it around and around, sometimes taking it off and rolling it between his other fingers before returning it to its place on his digit, covering the pale soft spot where it constantly rested. His right hand was occupied with an item as well, every so often bringing the now half-empty bottle of whiskey to his lips for long drags of the fiery liquor. Some nights it only took him a few pulls from the bottle to knock back into unconsciousness, while other nights required full bottles before his body and mind would succumb. Tonight was looking to be a full-bottle night.

Not that he ever rested. The booze may put him to sleep, but even when he was too blacked out to remember his own name while conscious, he relived the nightmare in perfect clarity every night, so that even in sleep he was robbed of rest.

Jonathan sat alone with his thoughts, just like always, when suddenly someone banged on the door to his apartment. And it was banging, a heavy fist insistently demanding his attention by beating down his door.

"Go 'way!" Jonathan shouted, not caring at all that his words were slurred.

"It's me, Jon. Open the door."

Jonathan recognized the voice outside his door. He still refused to move. "Leave me be, Roland," he was still shouting at the door, but his voice lost some of its heat.

There was a click followed by the sound of his crappy door scraping along the floor of his entryway, and Jonathan's oldest and quite frankly only friend walked into the room.

"The hell, Roland? I wouldn't think one of the city's finest detectives would stoop to picking locks to occupied apartments,"

Roland lifted one hand, revealing a small key. "You gave me a key, remember?"

Jonathan grunted, taking another pull from the bottle. It was down to a quarter now.

Roland stood there silently for a moment. Finally, he walked around the back of Jonathan's chair and stood in front of the window, Jonathan to look at him.

"What?"

"Aren't you going to ask me why I'm here?"

"Why bother? You're going to tell me anyway," Jonathan lifted the bottle once more.

Roland grabbed it on its way to his friend's lips, smoothly taking it from the drunken man's hand. Jonathan stood up, reaching for it, ready to knock his friend around for taking the only thing that gave him some measure of solace.

Roland put one hand on Jonathan's chest and gave him a shove, knocking his inebriated friend back into his chair.

"You're having the nightmares again," he said.

"So?" Jonathan managed to glare, even though his eyes were glazed.

"You promised me after the last case you'd see someone who could help you, Jon. You said you were getting better and you wanted to stay that way. And you told me you'd stop with _this_," he said, giving the bottle a slight shake. "You lied."

"The fuck do you care?" Jonathan growled. "What I do in my own home is my business. And for your _information_, I didn't lie. I did see a shrink. Fucking quack told me I was fixating. Told me I had to let it go, move on. That enough time had passed for me to mourn." Jonathan rose, pacing the room on unsteady feet and shaky legs. "The fuck does he know?"

Roland watched Jonathan pace, his steely blue eyes following his friend without emotion. His silence drove Jonathan insane, and he continued in his tirade.

"He doesn't know, he _can't know,_ how it felt. I held her in my arms, I was _right there,_ and I couldn't save her, couldn't protect her, couldn't even say goodbye…" he slumped against a wall. "The quack doesn't know how it feels, Roland. How can I ever let her go? She was everything…"

Roland set the bottle down on the windowsill and walked to his friend, setting a hand on Jonathan's shoulder.

"You're right, Jon. I know how much she meant to you," He gave Jonathan's shoulder a squeeze, hard enough to earn another bleary glare. Jonathan didn't realize that's what his friend wanted until their eyes met, and Roland continued, "But she's _gone._ She's gone, though she didn't deserve to leave. And as faithful as you are to her memory, it won't bring her back. Nothing will. But just because she was taken doesn't mean you have to martyr yourself. How would she feel if she saw you like this?"

The words stung. Jonathan felt the tears forming in his eyes. He shook his head viciously, then reached up slapped away Roland's hand. "Why are you here?"

Roland hooked his hands under Jon's arms and lifted him to his feet. "I need your help, Jon. It's for a case. So go dunk your head in some cold water and get dressed. We leave in ten minutes."

"I thought the city didn't want you working with me anymore." Jonathan said, looking for an excuse.

"This time it's different, Jon. You'll see. Now are you going to go sober up or am I going to have to do it for you?"

Roland wasn't usually the type to push people around, not even Jon when he was drunk. Jon supposed it must be something pretty unusual to inspire this attitude in his friend.

"Fine. But you owe me another bottle of booze for this."

True to his word, Roland drug Jonathan out of his apartment ten minutes later, with the half-sober man shucking into his trench coat as he was shoved unceremoniously to the stairs.

"Jesus, Roland. Slow the hell down, will you? Let a guy get his bearings before you throw him down the stairs."

"You wouldn't need pushing if your back teeth weren't swimming in scotch," Roland snapped back. "Now hurry up, we need to get there as fast as we can. This is important."

Jonathan started down the stairs, keeping one hand on the thin railing at all times. "What happened that you guys need me there in such a hurry?"

"You'll see when you get there, Jon."

Jonathan grunted, already tired of hearing that phrase. It was obvious that he wasn't happy with Roland's verbal discretion, and it was equally obvious that Roland wasn't going to spill no matter what Jonathan said, so he settled for sullen silence as they thumped their way down three flights of stairs.

They exited the building, stepping onto the rain-soaked sidewalk. Jonathan flipped up the collar of his coat so that it touched the back of his hat, the small brim blocking most of the falling water, the coat catching the rest and keeping it from trickling down the back of his neck. Jonathan felt Roland nudge him to the left, and they both started down the sidewalk, which was practically deserted in the rain.

Jonathan almost started complaining about being wet and cold and why were they out in the fucking rain, but he stopped himself when he saw Roland was leading him to a police car. It was a solid build, all heavy steel in flowing lines, with the exposed wheels and solid body that was the standard for the time. They climbed in, and Roland started the car and hit the roads with the self-assurance that only a man with a mission could have. Jonathan still wasn't happy, but he took some comfort at being out of the rain.

Now that he didn't have to duck his head to shelter himself, Jonathan found himself staring through the car window, losing himself in the sight of the city, just like he did while he was in his apartment. He'd always loved the skyline, the silhouettes of the buildings punctuated by neon lights and dark alleys.

Memories returned unbidden then, flashes of smiles and hand holding while taking long walks, walks with no destination, whose only objective was to see more of their home city and spend time with the one they loved. The images in Jonathan's head were crisp, clean, like they had happened only yesterday, but the scenes playing out in his head lacked all sensations of sound or smell. He could still see her, though, see her smile as she laughed at some stupid joke he had made, see her tuck stray hair behind her ear to keep it out of her face, see her hold out her hand to him, a silent invitation he took without hesitation.

And for the first time ever, when he remembered touching her hand, he could see the contact, but _he couldn't feel it. _

Jonathan snapped back to reality in a rush, his head snapping back slightly as if he'd smacked lightly across the cheek. Roland noticed the twitch, sparing a short glance at his passenger before returning his attention to the road, continuing along at the same smooth rate through the rain-soaked night.

Jonathan schooled his expression back to one of disinterest, staring resolutely forward, pointedly ignoring the view he'd been enjoying previously. He refused to see those memories again; he began counting numbers in his head, starting with two and doubling them over and over, going as high as he could, restarting the process when he made a mistake. It kept his mind busy, driving away the need to process what his subconscious had just thrown in his face.

Jonathan's mathematical coping mechanism kept him distracted until Roland stopped the car in front of a shabby apartment complex at the edge of the district. Jonathan looked through the left side of the car, the same direction their destination building faced, and could make out the vague shadow of the Wall.

"Lovely bit of scenery," Jonathan remarked to Roland. "A view like that probably makes the rent nice and cheap."

Roland grunted an affirmation. He'd never been fond of anything having to do with the Wall, and it showed in the tightness of his shoulders and his monosyllabic responses. Roland climbed out of the car, and Jonathan followed, the two of them walking together into the building.

They passed other uniformed officers in the first floor of the apartment building, most of them ignoring the duo entirely. Those who didn't gave slight nods to Roland, and looks of barely contained disgust at Jonathan.

"I see I'm still _persona non grata _with the force. So I ask again, Roland. What the hell am I doing here?"

Roland said nothing, and turned for the stairs, giving Jonathan no choice but to follow. Roland took the steps two at a time, and Jonathan struggled to keep up. The haziness from the booze had lessened, but it definitely wasn't gone.

They climbed at least a dozen flights of stairs, with Roland barely slowing the entire time. Jonathan huffed and puffed, his chest burning with the passage of air and his knees aching steadily. _What the hell,_ Jonathan thought. _When did my knees become something that hurts?_

Finally, on the thirteenth floor of the apartment, Roland stepped through a door instead of turning up the next flight, much to Jonathan's relief. The doorway led them into a long hallway, with faded green doors lining the walls at regular intervals, and a god awful patterned carpet covering the floor. Roland led Jonathan down the hallway, then stopped abruptly at the last door on the left. The faded gold lettering on the door read 139. Roland knocked twice, and the door opened from within.

As soon as the door cracked open, a horrid stench blasted right into Jonathan's face. It smelled of human waste, and the sickly sweet smell of death. The scent hit him hard enough that combined with his stomach of booze, Jonathan had to lean against the wall of the hallway, eyes closed and hands against the cheap wallpaper, taking deep breaths to calm his stomach before he retched. Roland waited, watching his friend while holding the door with one hand.

After a tense minute, Jonathan once again adopted his bland look of indifference and followed Roland into the room. A couple of other detectives were still in the room, taking pictures of a body on the floor, talking quietly with one another, and searching idly through the room.

Jonathan followed Roland over to the body, looking around the room as he did. The interior was very Spartan, the furniture looking well-worn but clean, and very few bits of ornamentation. The room screamed single male, which would explain why it was only one dead guy on the floor. Nothing seemed out of place in the main room other than the aforementioned body.

Roland cleared his throat once, and all of the detectives stopped what they were doing and looked to him. "Clear out, everyone. If you haven't gotten enough yet, tough shit. Wait downstairs."

The detectives had apparently been waiting for that order, because they all collected their gear and shuffled out without a word of protest. They all looked shaken, which in Jonathan's mind didn't track. These guys were seasoned homicide detectives. They'd seen much worse than this stiff could offer. What about this had them spooked?

Jonathan regretted asking that as soon as it crossed his mind.

"Ok Roland, I'm officially even more confused. You show up, drag me out of my apartment, schlep me across town to a _different _ apartment, only this one has one relatively normal dead guy surrounded by a bunch of jaded cops who look like they've seen the boogeyman. For the last time, what the fuck is going on?"

Roland's eyes had the same bleak look in them that the other detectives had. He motioned to the corpse. "Take a look," he said. "You're a smart guy. Tell me what you see and if it explains our apprehension."

Jonathan fumed in his head. Why the hell was Roland being so cagey? Normally he'd lay out everything plain, in an effort to be as concise and efficient as possible. This was not like him at all.

Still, Jonathan supposed looking couldn't hurt. He knelt down next to the corpse, idly taking off his hat and holding it out behind him. When Roland didn't take it, he shook it in his hand, clearing his throat while refusing to look back. He heard a long suffering sigh and felt the hat get snatched out of his hand. "Easy, Jesus. I like that hat," he said, still refusing to take his eyes away from the dead body. It was a man, maybe in his mid to late thirties. He was wearing a black suit, scratch that, a black uniform, with one sleeve ripped off. He was of solid build, a hair under six feet tall, and packed both muscle and a decent chunk of fat on him. His hair was a dirty blond, and was thinning and receding. He was lying on his back, his eyes bulging from his head, his face locked in rictus, fear and what might be confusion permanently etched into his final expression.

Looking around his head, Jonathan discovered what must have killed this poor bastard. His neck was covered in red and black bruises, covering the front of his neck and reaching around almost to the vertebrae in the back. But what looked like one massive line was, upon closer inspection, three thick lines surrounding the late man's throat. _What the hell kind of person strangles a guy three times from three different angles_? Jonathan thought, looking closer. Almost instantly he wished he hadn't. The man's throat wasn't just bruised from strangulation, it was fucking _crushed._ The man's windpipe had collapsed under the pressure it had been put under, and the soft tissue and cartilage was compressed and broken.

Jonathan sat back, looking up at Roland for the first time during his inspection. "What the hell happened here, Roland? Three separate but _large_ ligature marks, a crushed neck, and no sign of a struggle? What could possibly do th…" Jonathan trailed off as an epiphany burst into life in his mind. He had been thinking that someone had snuck up on this poor bastard, wrapping a belt or something around his neck and riding him to the floor, choking him and killing him. The separate marks had come when the strangling cord had slipped, which didn't quite add up. Instead, a new image popped into Jonathan's head. A massive, three-fingered hand holding the man aloft, while the thick digits squeezed harder and harder, cutting off air and crushing the life out of their victims. Jonathan had heard brutal, alien laughter before, and he imagined it happening here, in this apartment, where people like this should have been safe from the foreign horror that had befallen this poor shmuck.

Roland could see the light bulb going off in Jonathan's head, and closed his eyes. "Dammit," he whispered, partly to himself. "I was hoping I was wrong about what happened here. But you think the same thing I do."

Jonathan stood up slowly, walking to the only window in the room. Looking out of the front of the building, at the looming, massive shape of the Wall in the distance. "This man was murdered. By one of _them."_


	2. Chapter 2

**Author's note: To everyone who's following this story, thank you so much. I'm new to fanfic, so the support is much appreciated. I'm not going to be able to post very often (Curse real-life responsibility), but I'm going to make every effort to keep working on Citadel Noire at every opportunity!**

Chapter two

Jonathan and Roland left the apartment, turning the crime scene back over to the uniformed officers in the lobby. They climbed back into Roland's car, neither man speaking; Jonathan's mind was fully engrossed in the mystery laid out before him, and Roland knew his friend well enough to simply let the gears grind away in Jonathan's head without interruption. Once they were back onto the rain-soaked streets, Jonathan finally pooped out of his reverie.

"How do you feel about being a soundboard for a bit, Roland?"

"I can grunt at appropriate points in the conversation to speed things along," Roland said.

"Good. Let's lay out the facts.

"We have one dead human, obviously choked to death by one of the aliens that live on the other side of the Wall. You know much about the different kinds of aliens over there?" Jonathan asked, without looking over, his thumb and forefinger idly stroking the stubble under his chin.

Roland had read all of the required reports on the aliens. But he knew Jonathan was going to launch into a detailed description anyway, so he simply said, "Remind me."

"You've got three main species, with a few others dashed about. The top three are the salarians, the asari, and the turians. The salarians are the clever ones. They're amphibious, look like frogs learned how to stand on their back legs but much skinnier. They're on average a little over five and half feet tall, with three fingered hands and scrawny limbs. Their eyes are usually monochromatic, and they have small cranial horns that sort of look more like thick but short antennae. They're almost all geniuses, the dumbest one of them could kick the ass of any man who ever lived in a game of chess, but they only live to be about forty years old. Rumor has it the leader of all the aliens over there is a salarian," Jonathan stopped for a breath, scratching idly at the back of his head before continuing.

"The asari are something else entirely. Somehow, the entire race is female. Which is weird. No one knows how they manage to make more of them. Not that you'll hear me complaining. They're all gorgeous, at least all the ones that I've seen. They look very similar to our own women, except their skin is usually a deep blue, sometimes purple tone. Instead of hair, they have these ridge-looking things that sweep backwards, sticking out past the end of their skulls by maybe an inch. They're diverse; some are ruthless and cunning, others compassionate and introverted. They're not too physically intimidating. Not weak by any means, but not hulking goliaths at all. They'd use wit and seduction before might any day. Some say they live for hundreds of years, and that they have the ability to move things with their minds. I kind of doubt that, though.

"Last are the turians. And if you thought the salarians look weird, you don't know jack about these freaks. Turians have always reminded me of the evolutionary link between dinosaurs and birds. Turians don't really don't have skin, they have more of a carapace. Their skin is usually a deep gray, but there have been turians with other colored skins too. They tend to have specific tattoos covering their faces, denoting their families or tribes or whatever. They don't have cheeks; they have a pair of mandibles on either side of their mouths that _really_ freak me the hell out. They have fringes like the asari, except much longer and spiny. They're rigid, ordered, and utterly tenacious. Like humans but with more structure. They also have three fingered hands, but they couldn't have the strength to crush a man's throat like that. Not unless they have some mutant version they've been hiding for the past twenty years."

Roland cleared his throat, interrupting the informational tirade. "That's the main three you mentioned. But you effectively ruled out all of them as you brought them up. So who _actually_ could've committed the murder?"

Jonathan spared his friend a deploring look for cutting him off. He didn't like it when his train of thought got derailed. Roland knew Jonathan would continue regardless, which he did after a moment. "There's only one group I've heard of that could possibly pull this off. They're rare even amongst the other aliens. They're called the krogan. They're huge. The smallest of them is about seven feet tall; even though the way they're built they're pretty hunched over. They weigh about eight hundred pounds, most of that raw muscle. They've got huge humps on their backs above their shoulders, which I assume they can use for sustenance if they're starving, kind of like camels. They're built to last in other ways, too. Their heads are broad and blunt, with their eyes widely spaced, like most prey animals like deer and cattle. Krogan have a bone plate on their foreheads about a foot in diameter and several inches thick, like the natural armor some dinosaurs have. The weirdest thing was when a krogan body was dissected back in the time before the Wall when we were all fighting. They have _redundant organs._ They body that was cut opening had two hearts, two nervous systems, and other duplicated vital organs, all completely natural. There were even some bullet wounds that were mostly healed, even though the krogan was shot only a couple of hours before the autopsy, indicating that they heal like freaks of nature even from serious wounds. One of them would have the strength to do that if it was angry enough, and they too have three fingers on each hand. If I were a betting man, I'd say we're looking for a krogan as our perp."

Roland digested this information in silence for a minute, while Jonathan continued running the facts through his rapidly clearing head. Finally, Roland spoke, his tone very clearly telling his idea of what they were up against. "So. You're telling me that our likely murderer is a massive, alien killing machine that is not only more than willing to kill, but also impossibly hard to capture do to the sheer toughness that is inherent in their body structure. Not to mention the fact that we can deduce nothing about the individual killer besides which race it likely is among a bunch of extraterrestrial beings that just showed up on our planet two decades ago."

Jonathan mused over his friend's commentary for a moment. "Yeah, that's pretty much got it covered."

Roland sighed, and then said something Jonathan never thought he'd hear his friend say: "Fuck me."

Roland drove them back to Jonathan's apartment building, parking his car right along the sidewalk in a spot Jonathan could've sworn wouldn't fit the vehicle. Roland pulled a thick satchel out of the back of his car, and then they walked back up the flights of stairs to Jonathan's apartment, both men lost in thought and walking by autopilot.

They walked inside, pulling chairs out from the dining table and sitting down. Jonathan grabbed a pair of brown-bottled beers from the fridge as Roland produced files from the satchel, depositing them on the table. He started sifting through them, separating them into piles as Jonathan sat down, popping the caps off the two bottles before setting one down in front of Roland, who barely even acknowledged it. He got like this when he was focused, Jonathan knew; Roland was like a parade horse with blinders on, his focus solely forward and unwavering.

Roland made two piles of folders, taking any extra files that weren't germane to the subject and tucking them back into the satchel. Then, he looked up at Jonathan for the first time since entering the apartment and took hold of his beer. "Which stack do you want?" he asked, taking a pull of the heavy stout in the bottle.

Jonathan looked at the two stacks. "What are my options?"

Roland pointed to the stack on his left, and said, "These are the files on the victim. Occupation, medical history, family records, et cetera." He pointed to the stack on his right, which was significantly smaller. "These are files containing everything we know about the aliens and how things are set up. Figure they could give us a leg-up on the investigation."

Jonathan was taken aback. "Wait, I thought the city didn't want anything to do with the aliens? You didn't say it, but I know that's why you called me in. You're probably getting shit from a hundred different people from higher up the food chain to cease and desist."

Roland grimaced, and asked, "How did you know that?"

"I didn't until you said that," Jonathan said, looking smug.

Roland said another word that his superiors wouldn't like him using in front of the press. "Fine," he said. "The city's official statement will say that the victim was killed, most likely a robbery gone wrong."

"And I suppose no one will mention the lack of human fingerprints, the strange ligature marks, and the obvious fact that nothing was taken from the apartment?"

"Not if any of us want to keep our jobs. Look, Jon. Internal Affairs is going to be on us like flies on shit, and if a cop goes anywhere near this case, they'll come down like a goddamn hammer. The city wants _nothing_ to do with anything on the other side of the wall. They'll keep the status quo alive as long as possible, and if that means that one dead guy doesn't get the justice he deserves, the powdered wigs downtown will be ok with that. As long as they can look in mirror each night and tell themselves that the boogeyman doesn't exist as long as the Wall doesn't come into view, they'll sleep well each night and do the same thing the next fucking morning."

Jonathan sat back, grabbing his beer off the table and blowing a huge sigh. The gears had been turning in his head as Roland had given his impromptu speech, filling in the blanks. Internal Affairs? That meant Jonathan needed to keep his nose clean, for Roland's sake. It also meant that if Jonathan got into any kind of trouble, there would be no cavalry coming over the hill to save the day. And if this investigation was going to be swept under the rug, Jonathan wouldn't be able to convince anyone of the truth without evidence that was completely and utterly irrefutable.

All in all, it meant that he had to throw himself into a situation in which he had no idea who the bad guys were, amongst the deadliest beings the world has ever seen, without any backup or official sanctioning, and he had to get everything tied into a nice little bow with no loose ends _on the first try,_ or he would end up dead or thrown under the rug with the rest of the trash the city didn't want to deal with.

Jonathan brought the beer to his lips, downing the last three quarters of the bottle in one go. He slammed the bottle back onto the table with a bang and said, "I'll take the files on the aliens. Then we switch."


End file.
